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Zheng L, Dong Y, Li B, Yin T, Liu C, Lin H. Simultaneous removal of high concentrations of ammonia nitrogen and calcium by the novel strain Paracoccus denitrificans AC-3 with good environmental adaptability. BIORESOURCE TECHNOLOGY 2022; 359:127457. [PMID: 35700895 DOI: 10.1016/j.biortech.2022.127457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/04/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
The novel Paracoccus denitrificans AC-3 strain was isolated and displayed outstanding purification capability for high concentrations of ammonia nitrogen (NH4+-N) and calcium (Ca2+). Meanwhile, the strain exhibited excellent environmental adaptability within a wide pH range and high levels of NH4+-N and Ca2+. Nitrogen balance analysis demonstrated that the pathways of NH4+-N removal consisted of 80.12% assimilation and 16.60% heterotrophic nitrification aerobic denitrification (HNAD). In addition, Ca2+ was removed by forming calcium carbonate (CaCO3) with carbonate (CO32-) and bicarbonate (HCO3-). CO32-and HCO3- were obtained from carbon dioxide (CO2) hydration, which was catalyzed by carbonic anhydrase (CA) secreted by strain AC-3. The alkaline environment for carbonate precipitation was provided by CA and HNAD. The resulting CaCO3 existed in the form of calcite and exhibited a unique morphology and elemental composition.
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Affiliation(s)
- Lili Zheng
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, Beijing 100083, China
| | - Yingbo Dong
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, Beijing 100083, China
| | - Bing Li
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, Beijing 100083, China
| | - Tingting Yin
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, Beijing 100083, China
| | - Chenjing Liu
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, Beijing 100083, China
| | - Hai Lin
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, Beijing 100083, China.
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2
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Abstract
Biomineralization in a starfish displays morphologically complex features.
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Affiliation(s)
- Stephen T Hyde
- School of Chemistry, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Fiona C Meldrum
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
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3
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Living materials fabricated via gradient mineralization of light-inducible biofilms. Nat Chem Biol 2020; 17:351-359. [PMID: 33349707 DOI: 10.1038/s41589-020-00697-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 10/15/2020] [Indexed: 11/08/2022]
Abstract
Living organisms have evolved sophisticated cell-mediated biomineralization mechanisms to build structurally ordered, environmentally adaptive composite materials. Despite advances in biomimetic mineralization research, it remains difficult to produce mineralized composites that integrate the structural features and 'living' attributes of their natural counterparts. Here, inspired by natural graded materials, we developed living patterned and gradient composites by coupling light-inducible bacterial biofilm formation with biomimetic hydroxyapatite (HA) mineralization. We showed that both the location and the degree of mineralization could be regulated by tailoring functional biofilm growth with spatial and biomass density control. The cells in the composites remained viable and could sense and respond to environmental signals. Additionally, the composites exhibited a maximum 15-fold increase in Young's modulus after mineralization and could be applied to repair damage in a spatially controlled manner. Beyond insights into the mechanism of formation of natural graded composites, our study provides a viable means of fabricating living composites with dynamic responsiveness and environmental adaptability.
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4
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Moreno B, DiCorato A, Park A, Mobilia K, Knapp R, Bleher R, Wilke C, Alvares K, Joester D. Culture of and experiments with sea urchin embryo primary mesenchyme cells. Methods Cell Biol 2019; 150:293-330. [PMID: 30777181 PMCID: PMC8273911 DOI: 10.1016/bs.mcb.2019.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Skeletogenesis in the sea urchin embryo gives rise to a pair of intricate endoskeletal spicules. Deposition of these skeletal elements in the early larva is the outcome of a morphogenetic program that begins with maternal inputs in the early zygote and results in the specification of the large micromere-primary mesenchyme cell (PMC) lineage. PMCs are of considerable interest as a model system, not only to dissect the mechanism of specific developmental processes, but also to investigate their evolution and the unrivaled level of control over the formation of a graded, mechanically robust, yet single crystalline biomineral. The ability to study gene regulatory circuits, cellular behavior, signaling pathways, and molecular players involved in biomineralization is significantly boosted by the high level of autonomy of PMCs. In fact, in the presence of horse serum, micromeres differentiate into PMCs and produce spicules in vitro, separated from the embryonic milieu. PMC culture eliminates indirect effects that can complicate the interpretation of experiments in vivo, offers superior spatiotemporal control, enables PMC-specific readouts, and is compatible with most imaging and characterization techniques. In this chapter, we provide an updated protocol, based on the pioneering work by Okazaki and Wilt, for the isolation of micromeres and subsequent culture of PMCs, as well as protocols for fixation and staining for fluorescent microscopy, preparation of cell cultures for electron microscopy, and the isolation of RNA.
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Affiliation(s)
- Bradley Moreno
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United States
| | - Allessandra DiCorato
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United States
| | - Alexander Park
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United States
| | - Kellen Mobilia
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United States
| | - Regina Knapp
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United States
| | - Reiner Bleher
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United States
| | - Charlene Wilke
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United States
| | - Keith Alvares
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United States
| | - Derk Joester
- Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United States.
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Pendola M, Jain G, Huang YC, Gebauer D, Evans JS. Secrets of the Sea Urchin Spicule Revealed: Protein Cooperativity Is Responsible for ACC Transformation, Intracrystalline Incorporation, and Guided Mineral Particle Assembly in Biocomposite Material Formation. ACS OMEGA 2018; 3:11823-11830. [PMID: 30320276 PMCID: PMC6173553 DOI: 10.1021/acsomega.8b01697] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/11/2018] [Indexed: 05/12/2023]
Abstract
The formation of the sea urchin spicule involves the stabilization and transformation of amorphous calcium carbonate (ACC) and assembly of ACC nanoparticle precursors into a mesoscale single crystal of fracture-resistant calcite. This process of particle assembly or attachment is under the control of a family of proteins known as the spicule matrix [Strongylocentrotus purpuratus (SpSM)] proteome. Recently, two members of this proteome, SpSM50 and the glycoprotein SpSM30B/C-G (in recombinant forms), were found to interact together via SpSM30B/C-G oligosaccharide-SpSM50 protein interactions to form hybrid protein hydrogels with unique physical properties. In this study, we investigate the mineralization properties of this hybrid hydrogel alongside the hydrogels formed by SpSM50 and SpSM30B/C-G individually. We find that the SpSM50 + SpSM30B/C-G hybrid hydrogel is synergistic with regard to surface modifications and intracrystalline inclusions of existing calcite crystals, the inhibition of ACC formation, and the kinetic destabilization of ACC to form a crystalline phase. Most importantly, the hybrid hydrogel phase assembles and organizes mineral particles into discrete clusters or domains within in vitro mineralization environments. Thus, the interactions of SpSM50 and SpSM30B/C-G, mediated by carbohydrate-protein binding, reflect the need for protein cooperativity for the ACC-to-crystalline transformation, intracrystalline void formation, and guided mineral particle assembly processes that are instrumental in spicule formation.
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Affiliation(s)
- Martin Pendola
- Laboratory
for Chemical Physics, Center for Skeletal and Craniofacial Biology, New York University, 345 E. 24th Street, New
York, New York 10010, United States
| | - Gaurav Jain
- Laboratory
for Chemical Physics, Center for Skeletal and Craniofacial Biology, New York University, 345 E. 24th Street, New
York, New York 10010, United States
| | - Yu-Chieh Huang
- Department
of Chemistry, Physical Chemistry, Universität
Konstanz, Universitätstrasse 10, Konstanz D-78457, Germany
| | - Denis Gebauer
- Department
of Chemistry, Physical Chemistry, Universität
Konstanz, Universitätstrasse 10, Konstanz D-78457, Germany
| | - John Spencer Evans
- Laboratory
for Chemical Physics, Center for Skeletal and Craniofacial Biology, New York University, 345 E. 24th Street, New
York, New York 10010, United States
- E-mail: (J.S.E.)
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6
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Jain G, Pendola M, Koutsoumpeli E, Johnson S, Evans JS. Glycosylation Fosters Interactions between Model Sea Urchin Spicule Matrix Proteins. Implications for Embryonic Spiculogenesis and Biomineralization. Biochemistry 2018; 57:3032-3035. [PMID: 29757633 DOI: 10.1021/acs.biochem.8b00207] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The formation of embryonic mineralized skeletal elements (spicules) in the sea urchin requires the participation of proteins, many of which may interact with one another and assist in the creation of an extracellular matrix wherein mineral formation takes place. To probe this, we created a sea urchin spicule recombinant model protein pair system wherein we tested the interactions between two major spicule proteins, SpSM50 and the glycoprotein, SpSM30B/C. Both proteins are strong hydrogelators that manipulate early and later events in mineral formation. We discovered that the anionic glycan moieties of SpSM30B/C are required for interaction with the SpSM50 protein and that these interactions are Ca(II)-independent. In addition, when these proteins form a complex, they create hybrid hydrogel particles that are physically distinct from their individual counterparts. Thus, glycan-mediated interactions play an important role in in vitro spicule protein assembly and most likely within the spicule itself.
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Affiliation(s)
- Gaurav Jain
- Laboratory for Chemical Physics, Center for Skeletal and Craniofacial Biology , New York University , 345 East 24th Street , New York , New York 10010 , United States
| | - Martin Pendola
- Laboratory for Chemical Physics, Center for Skeletal and Craniofacial Biology , New York University , 345 East 24th Street , New York , New York 10010 , United States
| | - Eleni Koutsoumpeli
- Department of Electronic Engineering , University of York , Heslington, York YO105DD , United Kingdom
| | - Steven Johnson
- Department of Electronic Engineering , University of York , Heslington, York YO105DD , United Kingdom
| | - John Spencer Evans
- Laboratory for Chemical Physics, Center for Skeletal and Craniofacial Biology , New York University , 345 East 24th Street , New York , New York 10010 , United States
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Jain G, Pendola M, Huang YC, Gebauer D, Evans JS. A Model Sea Urchin Spicule Matrix Protein, rSpSM50, Is a Hydrogelator That Modifies and Organizes the Mineralization Process. Biochemistry 2017; 56:2663-2675. [DOI: 10.1021/acs.biochem.7b00083] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Gaurav Jain
- Laboratory
for Chemical Physics, Center for Skeletal and Craniofacial Biology, New York University, 345 East 24th Street, New York, New York 10010, United States
| | - Martin Pendola
- Laboratory
for Chemical Physics, Center for Skeletal and Craniofacial Biology, New York University, 345 East 24th Street, New York, New York 10010, United States
| | - Yu-Chieh Huang
- Physical
Chemistry, Department of Chemistry, Universität Konstanz, Universitätstrasse
10, D-78457 Konstanz, Germany
| | - Denis Gebauer
- Physical
Chemistry, Department of Chemistry, Universität Konstanz, Universitätstrasse
10, D-78457 Konstanz, Germany
| | - John Spencer Evans
- Laboratory
for Chemical Physics, Center for Skeletal and Craniofacial Biology, New York University, 345 East 24th Street, New York, New York 10010, United States
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8
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Jain G, Pendola M, Rao A, Cölfen H, Evans JS. A Model Sea Urchin Spicule Matrix Protein Self-Associates To Form Mineral-Modifying Protein Hydrogels. Biochemistry 2016; 55:4410-21. [PMID: 27426695 DOI: 10.1021/acs.biochem.6b00619] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In the purple sea urchin Strongylocentrotus purpuratus, the formation and mineralization of fracture-resistant skeletal elements such as the embryonic spicule require the combinatorial participation of numerous spicule matrix proteins such as the SpSM30A-F isoforms. However, because of limited abundance, it has been difficult to pursue extensive biochemical studies of the SpSM30 proteins and deduce their role in spicule formation and mineralization. To circumvent these problems, we expressed a model recombinant spicule matrix protein, rSpSM30B/C, which possesses the key sequence attributes of isoforms "B" and "C". Our findings indicate that rSpSM30B/C is expressed in insect cells as a single polypeptide containing variations in glycosylation that create microheterogeneity in rSpSM30B/C molecular masses. These post-translational modifications incorporate O- and N-glycans and anionic mono- and bisialylated and mono- and bisulfated monosaccharides on the protein molecules and enhance its aggregation propensity. Bioinformatics and biophysical experiments confirm that rSpSM30B/C is an intrinsically disordered, aggregation-prone protein that forms porous protein hydrogels that control the in vitro mineralization process in three ways: (1) increase the time interval for prenucleation cluster formation and transiently stabilize an ACC polymorph, (2) promote and organize single-crystal calcite nanoparticles, and (3) promote faceted growth and create surface texturing of calcite crystals. These features are also common to mollusk shell nacre proteins, and we conclude that rSpSM30B/C is a spiculogenesis protein that exhibits traits found in other calcium carbonate mineral modification proteins.
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Affiliation(s)
- Gaurav Jain
- Laboratory for Chemical Physics, Center for Skeletal and Craniofacial Biology, New York University , 345 East 24th Street, New York, New York 10010, United States
| | - Martin Pendola
- Laboratory for Chemical Physics, Center for Skeletal and Craniofacial Biology, New York University , 345 East 24th Street, New York, New York 10010, United States
| | - Ashit Rao
- Department of Chemistry, Physical Chemistry, Universität Konstanz , Universitätstrasse 10, D-78457 Konstanz, Germany
| | - Helmut Cölfen
- Department of Chemistry, Physical Chemistry, Universität Konstanz , Universitätstrasse 10, D-78457 Konstanz, Germany
| | - John Spencer Evans
- Laboratory for Chemical Physics, Center for Skeletal and Craniofacial Biology, New York University , 345 East 24th Street, New York, New York 10010, United States
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9
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Chang IYT, Joester D. Large Area Cryo-Planing of Vitrified Samples Using Broad-Beam Ion Milling. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2015; 21:1616-1621. [PMID: 26455924 DOI: 10.1017/s143192761501510x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
On account of its excellent resolution and high throughput, cryoSEM imaging has recently seen resurgence. In this work, we report on the development of cryogenic triple ion gun milling (CryoTIGM™), a broad ion beam milling technique for cryo-planing of vitrified, "frozen-hydrated" specimens. We find that sections prepared with CryoTIGM™ are smooth over exceptionally large areas (~700,000 µm2), and reveal ultrastructural details in similar or better quality than freeze-fractured samples.
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Affiliation(s)
- Irene Y T Chang
- Department of Materials Science and Engineering,Northwestern University,2220 Campus Drive,Evanston,IL 60208,USA
| | - Derk Joester
- Department of Materials Science and Engineering,Northwestern University,2220 Campus Drive,Evanston,IL 60208,USA
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10
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Cryo-planing of frozen-hydrated samples using cryo triple ion gun milling (CryoTIGM™). J Struct Biol 2015; 192:569-579. [PMID: 26549007 DOI: 10.1016/j.jsb.2015.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 11/23/2022]
Abstract
Cryo-SEM is a high throughput technique for imaging biological ultrastructure in its most pristine state, i.e. without chemical fixation, embedding, or drying. Freeze fracture is routinely used to prepare internal surfaces for cryo-SEM imaging. However, the propagation of the fracture plane is highly dependent on sample properties, and the resulting surface frequently shows substantial topography, which can complicate image analysis and interpretation. We have developed a broad ion beam milling technique, called cryogenic triple ion gun milling (CryoTIGM™ ['krī-ə-,tīm]), for cryo-planing frozen-hydrated biological specimens. Comparing sample preparation by CryoTIGM™ and freeze fracture in three model systems, Baker's yeast, mouse liver tissue, and whole sea urchin embryos, we find that CryoTIGM™ yields very large (∼700,000 μm(2)) and smooth sections that present ultrastructural details at similar or better quality than freeze-fractured samples. A particular strength of CryoTIGM™ is the ability to section samples with hard-soft contrast such as brittle calcite (CaCO3) spicules in the sea urchin embryo.
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11
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Alessandri I. Enhancing Raman Scattering without Plasmons: Unprecedented Sensitivity Achieved by TiO2 Shell-Based Resonators. J Am Chem Soc 2013; 135:5541-4. [DOI: 10.1021/ja401666p] [Citation(s) in RCA: 184] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ivano Alessandri
- INSTM and
Chemistry for Technologies Laboratory, University of Brescia, via Branze 38, 25123 Brescia,
Italy
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